At this point I tried to copy only those files that were NO LONGER part of the new firmware
4) cp -r -u -T /var/sda1/usr /usr

I wasn't convinced that I had done that correctly, so to be safe, I untared my backup of /usr
5) tar -xzvf /usr.tar.gz /usr

Perhaps simply copying the old version of /usr over top of the new version and then untaring like my last step is the easiest way to go. It ensures that you have all of the old files that were removed, plus all of the new files.